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- PDB-3f42: Crystal structure of uncharacterized protein HP0035 from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 3f42
TitleCrystal structure of uncharacterized protein HP0035 from Helicobacter pylori
Componentsprotein HP0035
Keywordsstructural genomics / unknown function / Helicobacter pylori Unknown-function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


bacterial nucleoid / DNA binding / cytoplasm
Similarity search - Function
Nucleoid-associated protein YbaB-like domain / Nucleoid-associated protein YbaB/EbfC family / YbaB/EbfC DNA-binding family / Ybab; Chain: A; / Nucleoid-associated protein YbaB-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoid-associated protein HP_0035
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsChang, C. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein HP0035 from Helicobacter pylori
Authors: Chang, C. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: protein HP0035
B: protein HP0035
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6726
Polymers22,4232
Non-polymers2484
Water2,558142
1
A: protein HP0035
B: protein HP0035
hetero molecules

A: protein HP0035
B: protein HP0035
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,34312
Polymers44,8474
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10390 Å2
ΔGint-39 kcal/mol
Surface area16390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.129, 99.566, 45.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

Detailstetramer by vector (x,y,z),(x,1-y,-z)

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Components

#1: Protein protein HP0035


Mass: 11211.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_0035 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Derivative / References: UniProt: O24876
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4K,0.2M Ammonium Acetate, 0.1M Sodium Citrate pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2008
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 19258 / Num. obs: 19185 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 29.06 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 50.3
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.68 / Num. unique all: 940 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.94 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 982 5.1 %RANDOM
Rwork0.17989 ---
all0.1819 19143 --
obs0.1819 19143 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 16 142 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221415
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9851898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5235192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57327.53669
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19415273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.438152
X-RAY DIFFRACTIONr_chiral_restr0.0960.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021059
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.5895
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58521415
X-RAY DIFFRACTIONr_scbond_it2.7793520
X-RAY DIFFRACTIONr_scangle_it4.4094.5475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 66 -
Rwork0.247 1312 -
obs-1378 99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9352.9033-0.89789.2069-2.54331.1736-0.10610.09740.059-0.30940.24760.11370.1215-0.1612-0.14150.021-0.0205-0.03060.02820.03650.070111.962546.2955-3.9623
21.5465-0.53170.07022.7154-1.03161.6649-0.01720.0692-0.0574-0.18170.1235-0.08170.2011-0.0581-0.10630.0485-0.016-0.01660.0149-0.0050.0288.339720.10329.884
32.2930.4652-0.76992.4539-1.92113.1087-0.0596-0.2531-0.09780.06840.0751-0.22990.16490.0456-0.01550.03720.0239-0.03040.0425-0.00610.05113.124316.759821.3262
43.5932-0.313-0.96044.9201-2.99123.75990.03290.07850.0669-0.19860.0598-0.13060.21310.1116-0.09270.02040.01060.01250.0224-0.01280.064420.016834.65333.0733
56.72013.6418-2.45033.8946-5.573910.40010.0766-0.31820.06070.1669-0.2362-0.1042-0.2030.30660.15960.1640.0075-0.04340.0519-0.07640.184824.44545.556212.4177
63.11620.5277-1.2012.2763-0.51043.24890.1314-0.50490.13930.2541-0.0853-0.222-0.27090.1428-0.04620.06110.0005-0.02430.1012-0.02810.03610.31828.329125.5941
73.36541.9744-0.50654.1439-0.7491.193-0.0077-0.1191-0.03050.02270.0491-0.01820.0283-0.1473-0.04140.01050.0111-0.00210.05110.00640.00241.670522.256220.4089
84.0181-0.2627-0.00959.2949-6.13334.83820.0645-0.17170.39780.5939-0.0708-0.0957-0.4394-0.04630.00630.05930.00240.0080.0224-0.01040.043412.450844.03413.7844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 24
2X-RAY DIFFRACTION2A25 - 55
3X-RAY DIFFRACTION3A56 - 77
4X-RAY DIFFRACTION4A78 - 92
5X-RAY DIFFRACTION5B8 - 24
6X-RAY DIFFRACTION6B25 - 55
7X-RAY DIFFRACTION7B56 - 77
8X-RAY DIFFRACTION8B78 - 91

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